Job ID = 11632680 sra ファイルのダウンロード中... Completed: 844063K bytes transferred in 25 seconds (270176K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 48118534 spots for /home/okishinya/chipatlas/results/rn6/SRX3360118/SRR6253224.sra Written 48118534 spots for /home/okishinya/chipatlas/results/rn6/SRX3360118/SRR6253224.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:25:36 48118534 reads; of these: 48118534 (100.00%) were unpaired; of these: 13314741 (27.67%) aligned 0 times 27803431 (57.78%) aligned exactly 1 time 7000362 (14.55%) aligned >1 times 72.33% overall alignment rate Time searching: 00:25:38 Overall time: 00:25:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5822305 / 34803793 = 0.1673 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 15 Feb 2019 07:27:18: # Command line: callpeak -t SRX3360118.bam -f BAM -g 2.15e9 -n SRX3360118.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360118.05 # format = BAM # ChIP-seq file = ['SRX3360118.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 15 Feb 2019 07:27:18: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:27:18: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:27:18: # Command line: callpeak -t SRX3360118.bam -f BAM -g 2.15e9 -n SRX3360118.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360118.20 # format = BAM # ChIP-seq file = ['SRX3360118.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 15 Feb 2019 07:27:18: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:27:18: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:27:18: # Command line: callpeak -t SRX3360118.bam -f BAM -g 2.15e9 -n SRX3360118.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360118.10 # format = BAM # ChIP-seq file = ['SRX3360118.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 15 Feb 2019 07:27:18: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:27:18: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:27:26: 1000000 INFO @ Fri, 15 Feb 2019 07:27:26: 1000000 INFO @ Fri, 15 Feb 2019 07:27:26: 1000000 INFO @ Fri, 15 Feb 2019 07:27:34: 2000000 INFO @ Fri, 15 Feb 2019 07:27:34: 2000000 INFO @ Fri, 15 Feb 2019 07:27:35: 2000000 INFO @ Fri, 15 Feb 2019 07:27:42: 3000000 INFO @ Fri, 15 Feb 2019 07:27:42: 3000000 INFO @ Fri, 15 Feb 2019 07:27:43: 3000000 INFO @ Fri, 15 Feb 2019 07:27:49: 4000000 INFO @ Fri, 15 Feb 2019 07:27:49: 4000000 INFO @ Fri, 15 Feb 2019 07:27:51: 4000000 INFO @ Fri, 15 Feb 2019 07:27:57: 5000000 INFO @ Fri, 15 Feb 2019 07:27:57: 5000000 INFO @ Fri, 15 Feb 2019 07:28:00: 5000000 INFO @ Fri, 15 Feb 2019 07:28:05: 6000000 INFO @ Fri, 15 Feb 2019 07:28:05: 6000000 INFO @ Fri, 15 Feb 2019 07:28:08: 6000000 INFO @ Fri, 15 Feb 2019 07:28:13: 7000000 INFO @ Fri, 15 Feb 2019 07:28:13: 7000000 INFO @ Fri, 15 Feb 2019 07:28:17: 7000000 INFO @ Fri, 15 Feb 2019 07:28:21: 8000000 INFO @ Fri, 15 Feb 2019 07:28:21: 8000000 INFO @ Fri, 15 Feb 2019 07:28:25: 8000000 INFO @ Fri, 15 Feb 2019 07:28:29: 9000000 INFO @ Fri, 15 Feb 2019 07:28:29: 9000000 INFO @ Fri, 15 Feb 2019 07:28:33: 9000000 INFO @ Fri, 15 Feb 2019 07:28:37: 10000000 INFO @ Fri, 15 Feb 2019 07:28:37: 10000000 INFO @ Fri, 15 Feb 2019 07:28:42: 10000000 INFO @ Fri, 15 Feb 2019 07:28:45: 11000000 INFO @ Fri, 15 Feb 2019 07:28:45: 11000000 INFO @ Fri, 15 Feb 2019 07:28:50: 11000000 INFO @ Fri, 15 Feb 2019 07:28:52: 12000000 INFO @ Fri, 15 Feb 2019 07:28:52: 12000000 INFO @ Fri, 15 Feb 2019 07:28:58: 12000000 INFO @ Fri, 15 Feb 2019 07:29:00: 13000000 INFO @ Fri, 15 Feb 2019 07:29:00: 13000000 INFO @ Fri, 15 Feb 2019 07:29:06: 13000000 INFO @ Fri, 15 Feb 2019 07:29:08: 14000000 INFO @ Fri, 15 Feb 2019 07:29:08: 14000000 INFO @ Fri, 15 Feb 2019 07:29:14: 14000000 INFO @ Fri, 15 Feb 2019 07:29:15: 15000000 INFO @ Fri, 15 Feb 2019 07:29:15: 15000000 INFO @ Fri, 15 Feb 2019 07:29:21: 15000000 INFO @ Fri, 15 Feb 2019 07:29:23: 16000000 INFO @ Fri, 15 Feb 2019 07:29:23: 16000000 INFO @ Fri, 15 Feb 2019 07:29:29: 16000000 INFO @ Fri, 15 Feb 2019 07:29:31: 17000000 INFO @ Fri, 15 Feb 2019 07:29:31: 17000000 INFO @ Fri, 15 Feb 2019 07:29:36: 17000000 INFO @ Fri, 15 Feb 2019 07:29:38: 18000000 INFO @ Fri, 15 Feb 2019 07:29:38: 18000000 INFO @ Fri, 15 Feb 2019 07:29:44: 18000000 INFO @ Fri, 15 Feb 2019 07:29:46: 19000000 INFO @ Fri, 15 Feb 2019 07:29:46: 19000000 INFO @ Fri, 15 Feb 2019 07:29:52: 19000000 INFO @ Fri, 15 Feb 2019 07:29:54: 20000000 INFO @ Fri, 15 Feb 2019 07:29:54: 20000000 INFO @ Fri, 15 Feb 2019 07:30:00: 20000000 INFO @ Fri, 15 Feb 2019 07:30:01: 21000000 INFO @ Fri, 15 Feb 2019 07:30:01: 21000000 INFO @ Fri, 15 Feb 2019 07:30:07: 21000000 INFO @ Fri, 15 Feb 2019 07:30:09: 22000000 INFO @ Fri, 15 Feb 2019 07:30:09: 22000000 INFO @ Fri, 15 Feb 2019 07:30:15: 22000000 INFO @ Fri, 15 Feb 2019 07:30:17: 23000000 INFO @ Fri, 15 Feb 2019 07:30:17: 23000000 INFO @ Fri, 15 Feb 2019 07:30:23: 23000000 INFO @ Fri, 15 Feb 2019 07:30:24: 24000000 INFO @ Fri, 15 Feb 2019 07:30:24: 24000000 INFO @ Fri, 15 Feb 2019 07:30:30: 24000000 INFO @ Fri, 15 Feb 2019 07:30:32: 25000000 INFO @ Fri, 15 Feb 2019 07:30:32: 25000000 INFO @ Fri, 15 Feb 2019 07:30:38: 25000000 INFO @ Fri, 15 Feb 2019 07:30:40: 26000000 INFO @ Fri, 15 Feb 2019 07:30:40: 26000000 INFO @ Fri, 15 Feb 2019 07:30:46: 26000000 INFO @ Fri, 15 Feb 2019 07:30:48: 27000000 INFO @ Fri, 15 Feb 2019 07:30:48: 27000000 INFO @ Fri, 15 Feb 2019 07:30:54: 27000000 INFO @ Fri, 15 Feb 2019 07:30:56: 28000000 INFO @ Fri, 15 Feb 2019 07:30:56: 28000000 INFO @ Fri, 15 Feb 2019 07:31:02: 28000000 INFO @ Fri, 15 Feb 2019 07:31:03: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:31:03: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:31:03: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:31:03: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:31:03: #1 total tags in treatment: 28981488 INFO @ Fri, 15 Feb 2019 07:31:03: #1 total tags in treatment: 28981488 INFO @ Fri, 15 Feb 2019 07:31:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:31:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:31:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:31:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:31:04: #1 tags after filtering in treatment: 28981352 INFO @ Fri, 15 Feb 2019 07:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:31:04: #1 finished! INFO @ Fri, 15 Feb 2019 07:31:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:31:04: #1 tags after filtering in treatment: 28981352 INFO @ Fri, 15 Feb 2019 07:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:31:04: #1 finished! INFO @ Fri, 15 Feb 2019 07:31:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:31:09: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:31:09: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:31:09: #1 total tags in treatment: 28981488 INFO @ Fri, 15 Feb 2019 07:31:09: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:31:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:31:10: #2 number of paired peaks: 53244 INFO @ Fri, 15 Feb 2019 07:31:10: start model_add_line... INFO @ Fri, 15 Feb 2019 07:31:10: #2 number of paired peaks: 53244 INFO @ Fri, 15 Feb 2019 07:31:10: start model_add_line... INFO @ Fri, 15 Feb 2019 07:31:10: #1 tags after filtering in treatment: 28981352 INFO @ Fri, 15 Feb 2019 07:31:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:31:10: #1 finished! INFO @ Fri, 15 Feb 2019 07:31:10: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:31:11: start X-correlation... INFO @ Fri, 15 Feb 2019 07:31:11: end of X-cor INFO @ Fri, 15 Feb 2019 07:31:11: #2 finished! INFO @ Fri, 15 Feb 2019 07:31:11: #2 predicted fragment length is 160 bps INFO @ Fri, 15 Feb 2019 07:31:11: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 15 Feb 2019 07:31:11: #2.2 Generate R script for model : SRX3360118.20_model.r INFO @ Fri, 15 Feb 2019 07:31:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:31:11: start X-correlation... INFO @ Fri, 15 Feb 2019 07:31:11: end of X-cor INFO @ Fri, 15 Feb 2019 07:31:11: #2 finished! INFO @ Fri, 15 Feb 2019 07:31:11: #2 predicted fragment length is 160 bps INFO @ Fri, 15 Feb 2019 07:31:11: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 15 Feb 2019 07:31:11: #2.2 Generate R script for model : SRX3360118.10_model.r INFO @ Fri, 15 Feb 2019 07:31:11: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:31:16: #2 number of paired peaks: 53244 INFO @ Fri, 15 Feb 2019 07:31:16: start model_add_line... INFO @ Fri, 15 Feb 2019 07:31:17: start X-correlation... INFO @ Fri, 15 Feb 2019 07:31:17: end of X-cor INFO @ Fri, 15 Feb 2019 07:31:17: #2 finished! INFO @ Fri, 15 Feb 2019 07:31:17: #2 predicted fragment length is 160 bps INFO @ Fri, 15 Feb 2019 07:31:17: #2 alternative fragment length(s) may be 160 bps INFO @ Fri, 15 Feb 2019 07:31:17: #2.2 Generate R script for model : SRX3360118.05_model.r INFO @ Fri, 15 Feb 2019 07:31:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:32:22: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:32:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:32:33: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:33:08: #4 Write output xls file... SRX3360118.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:33:08: #4 Write peak in narrowPeak format file... SRX3360118.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:33:09: #4 Write summits bed file... SRX3360118.20_summits.bed INFO @ Fri, 15 Feb 2019 07:33:09: Done! pass1 - making usageList (105 chroms): 6 millis pass2 - checking and writing primary data (20922 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:33:19: #4 Write output xls file... SRX3360118.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:33:19: #4 Write peak in narrowPeak format file... SRX3360118.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:33:19: #4 Write summits bed file... SRX3360118.10_summits.bed INFO @ Fri, 15 Feb 2019 07:33:19: Done! pass1 - making usageList (130 chroms): 6 millis pass2 - checking and writing primary data (27271 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:33:20: #4 Write output xls file... SRX3360118.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:33:21: #4 Write peak in narrowPeak format file... SRX3360118.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:33:21: #4 Write summits bed file... SRX3360118.05_summits.bed INFO @ Fri, 15 Feb 2019 07:33:21: Done! pass1 - making usageList (149 chroms): 7 millis pass2 - checking and writing primary data (32122 records, 4 fields): 45 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。